SAXSdb — 3vmf

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongation factor 1-alpha

Aeropyrum pernix

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptide chain release factor subunit 1 × 1 （Q9YAF1） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EF1A_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–440； UniProt 1–437

Peptide chain release factor subunit 1

Aeropyrum pernix

UniProt Q9YAF1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Elongation factor 1-alpha × 1 （Q9YAV0） GUANOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RF1_AERPE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–373； UniProt 1–373

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3vmf
Deposition date deposition_date	2011-12-12
Structure title title	Archaeal protein
Keywords keywords	translation termination, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3vmf__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3vmf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vmf__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.40 Å
Rg (electron density)	32.07 Å
Total Rg	32.54 Å
Atom count	5999
Residues	778
Excluded volume	108020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vmf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Elongation factor 1-alpha
Molecular weight formula_weight	49016.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6161

GSHMAEKPHMNLVVIGHVDHGKSTLVGHLLYRLGYIEEKKLKELEEQAKSRGKESFKFAWILDKMKEERERGITIDLTFMKFETKKYVFTIIDAPGHRDFVKNMITGASQADAAILVVSARKGEFEAGMSTEGQTREHLLLARTMGIEQIIVAVNKMDAPDVNYDQKRYEFVVSVLKKFMKGLGYQVDKIPFIPVSAWKGDNLIERSPNMPWYNGPTLVEALDQLQPPAKPVDKPLRIPVQNVYSIPGAGTVPVGRVETGVLRVGDKVVFMPPGVVGEVRSIEMHYQQLQQAEPGDNIGFAVRGVSKSDIKRGDVAGHLDKPPTVAEEFEARIFVIWHPSAITVGYTPVIHVHTASVSSRIIEIKAKLDPKTGQVVEQNPQFLKAGDAAIVRFKPVKPLVVEKFSEIPQLGRFAMRDMNRTVGIGIVTDVKPAKVDIKAK

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide chain release factor subunit 1
Molecular weight formula_weight	42005.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSQGRLEERLTISKRELARLLKELKKWSAPATVLLSLYIPPGRPLSDVMTLLRQEYSITDNIKLKRTRQAVKRALSAAMDRLQMLTSTPPNGLVLFCGEDMSTGKFECFMFSPPEPIRVFYYRTDKRFITDFLEDMVEDNNAIGIIIVERDQATIGLLKGARLEVLKELEGFVPGKHKMGGQSQRRYERIIEQMVDEFFKKVGEEASNLLVPLAEKGVLKGVIVAGPGLAKQEFVEGNYLDYRLKKILAPELVDVAYQGLQGLKEAVMKAEKVVEAQMYRDAVNAMEEFKLHLAKGTGMIVYGEKDVEAALEMGAVKTLLIHESREDLEEWVEKAKSSGAQVIVVPESLAEAEWFLKTFGGLAGILRFRISTV

Source Source

Source organism organism	Aeropyrum pernix
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3vmfa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

Domain ID domain_id	d3vmfa2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.0 — automated matches

Domain ID domain_id	d3vmfa3
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family family	b.44.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3vmfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3vmfA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3vmfA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	3vmfB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	960 — Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A
Homologous superfamily homologous superfamily	10 — eRF1 domain 1

Domain ID domain_id	3vmfB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	60 — eRF1 domain 2

Domain ID domain_id	3vmfB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

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Unit-cell length a length_a	176.567 Å
Unit-cell length b length_b	55.169 Å
Unit-cell length c length_c	90.689 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.61 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.498 Å
R factor r_factor	0.2042
R_work r_work	0.2013
R_free r_free	0.2606

Archaeal protein

1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongation factor 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Peptide chain release factor subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3vmf__assembly_1__model_1

3vmf__assembly_1__model_1 | I(q)

3vmf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Archaeal protein

1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongation factor 1-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptide chain release factor subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3vmf__assembly_1__model_1

3vmf__assembly_1__model_1 | I(q)

3vmf__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)